In this project, we implement molecular dynamics to simulate the diffusion behavior of small molecules, especially drug molecules, inside an amorphous polymer matrix. From the simulation data, we can calculate the diffusion coefficient of the penetrants. The benefit of such simulation is that we could estimate the diffusion coefficient of small molecules through a desired polymer system without doing experiments which, in many instances, require the use of hazardous radiolabeled drug molecules. This can avoid inconvenient experiment and save time, effort and facilities. Futhermore, the simulation could give us the molecular level understanding on the diffusion process. This understanding is very important in establishing the interrelationship among the drug structure, polymer structure, and diffusion coefficients. Such information can be used to design new polymeric systems for controlled drug release.